Debur and polish the .040 crank just as it is and put the new .040 bearings back in. You don't have a bunch of lines cut into the crank, it will polish up and give you the .002 oil film barrier you need to run it.
Crankshafts are tough as long as they are not scored, burned, or gouged.
As Crazy as it sounds I would take a shot at saving those .040 pistons too. Debur the top outter crown above the top ring groove, pick out any hardened steel fragments and get rid if any high spots. Clean all the ring grooves and see what you got.
As one of my mentors told me, go ahead and try, the worst you can do is screw it up.
Find a new or used set of .040 pistons, can put them in too.